Currently, there is a shift to biological systems for production of a variety of chemicals and fuels, and a wide assortment of organisms are and will be used, most of them microbes, with an increasing tendency towards photosynthetic organisms (Dismukes 2008). The ability to grow robustly, the ability to resist toxic compounds, abiotic stresses, changes in growth conditions, and efficient production of the materials and compounds of interest, are desirable properties of these organisms.
Yeasts are widely employed as fermentation organisms for the production of ethanol, butanol, isobutanol and other alcohols, and a variety of commodity and fine chemicals. Yeasts used for bio-production include the baker's yeast Saccharomyces cerevisiae; other Saccharomyces species; Schizosaccharomyces pombe; Kluyveromyces species such as K. lactis, K. marxianus and K. thermotolerans; Candida species such as C. albicans, C. glabrata, C. stellate, C. tropicalis, C. dubliniensis and C. keroseneae; Pichia species such as P. angusta, P. anomala, P. membranifaciens and P. pastoris; oleaginous yeasts such as Yarrowia lipolytica; and other yeast species such as Dekkera/Brettanomyces species, Brettanomyces bruxellensis, Torulaspora delbrueckii and Zygosaccharomyces bailii. 
Many biological production systems using S. cerevisiae and other eukaryotic and prokaryotic production hosts depend on resistance and tolerance properties of the production organisms for efficient production of the desired chemical. For example, many fermentation processes are exothermic and require the removal of heat or cooling of bioreactors to ensure the continued viability and productivity of the organism used for fermentation. Media used for production can have low or high pH values (i.e. pH<5.0 for low pH values, pH>9.0 for high pH values) due to acidic or basic pre-treatment processes that were used for the production of sugars used in the fermentation. Alternatively, media used in fermentation can contain salts (i.e. sodium chloride) resulting from neutralization with bases or acids of the acids and bases used in the pre-treatment processes. Because the growth of many species of microbes, including many yeasts, is inhibited by heat, salt, low pH or high pH, it is often necessary to employ microbes that are naturally tolerant or resistant to these abiotic stresses, or to engineer sensitive strains and species of microbes for higher levels of tolerance or resistance.
Alcohols, such as ethanol, butanol and isobutanol are common products of fermentation processes employing yeasts and other microbes. Alcohols are toxic compounds and can be tolerated by yeasts and other microbes only in limited concentrations. Although some ethanol-producing yeast species are naturally resistant to ethanol (for example Saccharomyces cerevisiae), higher ethanol tolerance is generally desirable in ethanol-producing industrial yeast strains to maximize the productivity of fermentation processes. Other alcohols such as butanol are highly toxic at low concentrations, and yeast species that are naturally resistant to these alcohols have not been found. It is therefore broadly desirable to enhance alcohol tolerance in yeast species used for the production of alcohols (Cakar 2012, Doğan 2014).
Furthermore, the feedstocks used in a variety of biological production systems, particularly those feedstocks derived from degradation of plant products, often contain elevated concentrations of salts, acetate, growth-inhibitory carbohydrates, or various toxic organic compounds derived from plant lignins. The ability of a production organism to tolerate the presence of these toxic compounds is a prerequisite for maximal productivities. In addition, the pH found in production systems may be outside the pH optimum for the production organism used, and the organism's ability to grow at pH values outside of its natural optimum may be important in certain production systems.
Renewable biomass, including lignocellulosic material and agricultural residues such as corn fiber, corn stover, corn cob, wheat straw, rice straw, and sugarcane bagasse, are low cost materials for bioethanol production. Dilute acid hydrolysis is commonly used in biomass degradation which hydrolyzes cellulose and hemicellulose fractions to increase fiber porosity to allow enzymatic saccharification and fermentation of the cellulose fraction. (Saha 2003). However, acid hydrolysis both acidifies the resulting mix of sugars and also generates inhibitory compounds that interfere with microbial growth and hinders subsequent fermentation. These compounds include aldehydes (such as furfural, 5-hydroxymethylfurfural, etc.), ketones, phenols, and organic acids (such as acetic, formic, levulinic acids, etc.). Two of the most potent inhibitors are furfural and 5-hydroxymethylfurfrual (5-hydroxymethylfurfrual referred to as “HMF” hereafter). Yeast growth can be reduced by the combination of furfural and HMF at concentrations as low as 5 mM (Liu 2004).
These inhibitors can be removed from the hydrolysate before its use in fermentation, using physical chemical or enzymatic steps and treatments. However, these additional steps add complexity to the production process, produce waste products, and add significantly to the production cost. Alternatively, species or strains of microbes or yeasts need to be used for fermentation that are resistant to inhibitors present in sugars derived from biomass and other sources, resistant to ethanol and other products of the fermentation, and/or tolerant of abiotic stresses such as high temperature, high salt and low pH that are frequently encountered during fermentation processes (Cakar 2012, Doğan 2014). Most yeast strains, including industrial strains, are susceptible to the growth-inhibiting compounds released by dilute acid hydrolysis pre-treatment (Martin 2003). Yet few yeast strains tolerant to inhibitors are available and the need for tolerant strains is well recognized (Klinke 2004, Zaldivar 2001, Nieves 2015).
Genetic or epigenetic changes in organisms can improve the organisms' performance and raise their productivities. Particularly useful is the introduction of nucleic acids that confer dominant traits. This implies that the functions performed by the introduced nucleic acids, whether they encode RNA or protein or perform another function in the cell or organism, alter or overrides the function performed by similar nucleic acids that are naturally present in the cell or organism.
The present disclosure describes 83 fusion polynucleotides that confer resistance and tolerance in S. cerevisiae to alcohols and to abiotic stresses such as heat, salt, and low pH. These fusion polynucleotides are generated by pairwise fusion of full length open reading frames present in the S. cerevisiae genome. They are useful for improving S. cerevisiae, other yeasts, and other production microbes and to raise the productivity of a variety of biological production systems.